That is more than double the number of dead listed earlier in the week.
Scores of troops and rescue workers were rescuing people trapped in floods in the southern Indian state. The state has been pounded by the worst monsoon rains in almost a century since August 8. Most of the deaths have been reported in drownings and landslides.
"The death toll has mounted to 164 from 67 on Wednesday. Almost all of the state's 14 districts are reeling under the devastating floods," an official at the state disaster management control room said by phone.
Helicopters and disaster management teams have been battling heavy rains since Thursday to reach flooded areas to free people stranded in homes or rooftops.
"With a let-up in the rains today, rescue operations have been intensified," the official said. The regional weather bureau has predicted heavy showers until Saturday.
People travel in a truck to a safer place as flood waters ravage the National Highway 47 in Ernakulam district of Kochi.
The number of people at the state-run relief camps has swollen to 223,139, even as domestic media reported that rainwater had started entering the shelters.
The floods have damaged hundreds of kilometres of roads and disrupted train and air services. The airport at Kochi, the busiest city in Kerala, will remain closed until August 26.
Prime Minister Narendra Modi is due to visit the state to oversee rescue and relief efforts.
India's monsoon season, between June and September, often sees heavy rains that are vital for agriculture, but which can cause immense destruction.
AFP adds: Vijayan's office on Friday posted a fresh warning for around 33 million residents of Kerala.
"Alert: all districts apart from Kasargod are under red alert... heavy rains may affect these 13 districts. Everyone please be cautious," his office tweeted.
Even before the latest warning, locals like Ajo Varghese have been posting desperate appeals for relief and rescue on social media.
"My family and neighbouring families are in trouble with flood in Pandanad Nakkada area in Alappuzha," Varghese said in a viral Facebook post.
"No water and food. Not able to communicate from afternoon. Mobile phones are not reachable and switch off. Please help... No rescue is available," he added.
A state official told AFP that apart from the new rainfall warnings, a breakdown of the local communication system was making it difficult for them to reach local people who may be in urgent need in the worst-affected areas.
The government says 10,000 kilometres of Kerala roads have been destroyed or damaged and tens of thousands of homes partially or completely damaged.
The gates of at least 34 major dams and reservoirs across the state have been opened in the last few days as water levels reached danger levels.
North and central Kerala has been worst-hit by the floods.
